PCNX1

pecanex 1

Basic information

Region (hg38): 14:70907405-71115382

Previous symbols: [ "PCNXL1", "PCNX" ]

Links

ENSG00000100731 ∙ NCBI:22990 ∙ OMIM:617655 ∙ HGNC:19740 ∙ Uniprot:Q96RV3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCNX1 gene.

• not_specified (20 variants)
• not_provided (18 variants)
• Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCNX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014982.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	5	10
missense			20	3	4	27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	8	9

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCNX1	protein_coding	protein_coding	ENST00000304743	36	207978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000139	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	1124	1.27e+3	0.887	0.0000687	15288
Missense in Polyphen		408	579.56	0.70398		6918
Synonymous	-0.375	474	464	1.02	0.0000236	4690
Loss of Function	8.35	17	113	0.151	0.00000674	1259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.000404	0.000397
East Asian	0.000218	0.000163
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000179	0.000176
Middle Eastern	0.000218	0.000163
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -1.95
• rvis_percentile_EVS: 1.87

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.466
• ghis: 0.595

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pcnx

Gene ontology

• Cellular component: integral component of membrane